3 Answers
3

It depends on what mods were present, but it is possible that the patcher wasn't compatible with them. See, though it is a patcher, if the files are modified too much, it can't tell where to insert code. This will cause it to overwrite those files.

Often, MCPatcher is updated to be compatible with specific mods, so those conflicts don't happen. However, this requires fine-tuning. It's probable that your mods weren't actually deleted, but were partially overwritten. This can either lead to a black-screen crash, or the mods simply appearing like they don't exist. The latter clearly happened in this case.

Though the patcher is great, I've found that patching it before I install other mods has never lead to conflicts, while patching it after sometimes has. Go figure.

Do you mean that the mods just didn't show up in MCPatcher, or you started up Minecraft and saw that they weren't installed any more? I noticed once or twice back when I used to use MCPatcher that sometimes it would just "forget" what mods I had installed, removing them from the list the next time I ran the program. The mods themselves were still installed, and would show up properly in-game, but MCPatcher couldn't tell.

I've since switched to the MultiMC Launcher since I've started running a few different instances of Minecraft and I needed a way to manage that.